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Sample GSM4081276 Query DataSets for GSM4081276
Status Public on Jul 29, 2020
Title Input_hnRNP-H1
Sample type SRA
 
Source name Melanoma
Organism Homo sapiens
Characteristics cell line: A375
cell type: Melanoma cell line
passages: 14-18
Extracted molecule total RNA
Extraction protocol HNRNPH1-RNA interactions were stabilized with UV crosslinking (254 nm, 400 mJ/cm2), followed by lysis in iCLIP lysis buffer, limited digestion with RNase I (Ambion), immunoprecipitation of HNRNPH1-RNA complexes with a HNRNPH1 primary antibody (Bethyl Labs #A300-511A, at 10 μg per mL of lysate). Sample was dephosphorylated with FastAP (ThermoFisher) and T4 PNK (NEB).
A barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB). RNA was reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter was then ligated to the cDNA fragment 3′ end. Sample was PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis. Samples were sequenced on the Illumina HiSeq 4000 platform.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description Ha3_11_input_S29_L007
Data processing Reads were adapter trimmed (cutadapt v1.9.dev1) and reads less than 18 bp were discarded.
Mapping was performed against the full human genome (hg38) including a database of splice junctions with STAR (v 2.4.0i). Uniquely mapping reads were then run through a custom-built PCR duplicate removal script.
eCLIP data sets with multiple in-line barcodes were merged at the usable read stage, and cluster identification was performed on usable reads using CLIPper11 (available at https://github.com/YeoLab/clipper/releases/tag/1.0).
Genome_build: hg38
Supplementary_files_format_and_content: file include Chromosome, Start position, Stop position, -log10(P-value), Log2 fold enrichment in eCLIP vs. input, Strand (+ or -)
 
Submission date Sep 16, 2019
Last update date Jul 29, 2020
Contact name Marco Mineo
E-mail(s) mmineo@bwh.harvard.edu
Phone 6175255656
Organization name Brigham and Women's Hospital
Street address 60 Fenwood Rd, BTM 8012
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL20301
Series (2)
GSE137489 Long noncoding RNA INCA1 regulates tumor interferon signaling.
GSE137526 Long noncoding RNA INCA1 regulates tumor interferon signaling [CLIP-seq]
Relations
BioSample SAMN12768233
SRA SRX6854810

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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